Genomic structures of SCN2A and SCN3A - Candidate genes for deafness at the DFNA16 locus

Norio Kasai, Kunihiro Fukushima, Yasuyoshi Ueki, Sai Prasad, Jennifer Nosakowski, Ken Ichi Sugata, Akemi Sugata, Kazunori Nishizaki, Nicole C. Meyer, Richard J.H. Smith

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

DFNA16 is a form of autosomal dominant non-syndromic hearing loss (ADNSHL) characterized by fluctuating progressive hearing impairment. Earlier, we mapped the deafness-causing gene to chromosome 2q23-24.3. In this paper, we describe fine mapping results using additional markers tightly linked to the DFNA16 candidate region. Critical recombinants at markers D2S354 and D2S124 define a 3.5-cM interval that contains the DFNA16 gene. Positional candidate genes include two members of the voltage-gated sodium channel family, the type 2 α subunit (SCN2A) and the type 3 α subunit (SCN3A). After showing that SCN2A is expressed in human fetal cochlea, we determined its genomic structure to facilitate mutation screening in our DFNA16 kindred. We also determined the genomic structure of SCN3A. These two genes are oriented head-to-head, with their 5′ ends separated by approximately 40 kb; their homology is 82% at the nucleotide level, and 85% for identities and 90% for positives at the amino acid level. They share similar genomic structures and have alternative splice isoforms that are developmentally regulated and highly conserved between species. Although no DFNA16-causing mutations were found in either gene, haplotype analysis with polymorphic markers in SCN2A introns further narrowed the candidate gene interval to the region flanked by D2S354 and STS SHGC-82894.

Original languageEnglish (US)
Pages (from-to)113-122
Number of pages10
JournalGene
Volume264
Issue number1
DOIs
StatePublished - Feb 7 2001
Externally publishedYes

Fingerprint

Deafness
Genes
Hearing Loss
NAV1.2 Voltage-Gated Sodium Channel
Mutation
Cochlea
Introns
Haplotypes
Autosomal Dominant 16 Deafness
Protein Isoforms
Nucleotides
Chromosomes
Amino Acids

Keywords

  • Autosomal dominant non-syndromic hearing loss
  • DFNA16
  • SCN2A
  • SCN3A

ASJC Scopus subject areas

  • Genetics

Cite this

Kasai, N., Fukushima, K., Ueki, Y., Prasad, S., Nosakowski, J., Sugata, K. I., ... Smith, R. J. H. (2001). Genomic structures of SCN2A and SCN3A - Candidate genes for deafness at the DFNA16 locus. Gene, 264(1), 113-122. https://doi.org/10.1016/S0378-1119(00)00594-1

Genomic structures of SCN2A and SCN3A - Candidate genes for deafness at the DFNA16 locus. / Kasai, Norio; Fukushima, Kunihiro; Ueki, Yasuyoshi; Prasad, Sai; Nosakowski, Jennifer; Sugata, Ken Ichi; Sugata, Akemi; Nishizaki, Kazunori; Meyer, Nicole C.; Smith, Richard J.H.

In: Gene, Vol. 264, No. 1, 07.02.2001, p. 113-122.

Research output: Contribution to journalArticle

Kasai, N, Fukushima, K, Ueki, Y, Prasad, S, Nosakowski, J, Sugata, KI, Sugata, A, Nishizaki, K, Meyer, NC & Smith, RJH 2001, 'Genomic structures of SCN2A and SCN3A - Candidate genes for deafness at the DFNA16 locus', Gene, vol. 264, no. 1, pp. 113-122. https://doi.org/10.1016/S0378-1119(00)00594-1
Kasai, Norio ; Fukushima, Kunihiro ; Ueki, Yasuyoshi ; Prasad, Sai ; Nosakowski, Jennifer ; Sugata, Ken Ichi ; Sugata, Akemi ; Nishizaki, Kazunori ; Meyer, Nicole C. ; Smith, Richard J.H. / Genomic structures of SCN2A and SCN3A - Candidate genes for deafness at the DFNA16 locus. In: Gene. 2001 ; Vol. 264, No. 1. pp. 113-122.
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abstract = "DFNA16 is a form of autosomal dominant non-syndromic hearing loss (ADNSHL) characterized by fluctuating progressive hearing impairment. Earlier, we mapped the deafness-causing gene to chromosome 2q23-24.3. In this paper, we describe fine mapping results using additional markers tightly linked to the DFNA16 candidate region. Critical recombinants at markers D2S354 and D2S124 define a 3.5-cM interval that contains the DFNA16 gene. Positional candidate genes include two members of the voltage-gated sodium channel family, the type 2 α subunit (SCN2A) and the type 3 α subunit (SCN3A). After showing that SCN2A is expressed in human fetal cochlea, we determined its genomic structure to facilitate mutation screening in our DFNA16 kindred. We also determined the genomic structure of SCN3A. These two genes are oriented head-to-head, with their 5′ ends separated by approximately 40 kb; their homology is 82{\%} at the nucleotide level, and 85{\%} for identities and 90{\%} for positives at the amino acid level. They share similar genomic structures and have alternative splice isoforms that are developmentally regulated and highly conserved between species. Although no DFNA16-causing mutations were found in either gene, haplotype analysis with polymorphic markers in SCN2A introns further narrowed the candidate gene interval to the region flanked by D2S354 and STS SHGC-82894.",
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